North-Western Himalayan Common Beans: Population Structure and Mapping of Quantitative Anthracnose Resistance Through Genome Wide Association Study

Abstract

Common bean ( Phaseolus vulgaris L.) is an important legume crop of north-western (NW) Himalayan region and the major disease that causes catastrophic loss to the crop is anthracnose, which is caused by Colletotrichum lindemuthianum . The pathogen is highly diverse and most of the commercial cultivars are susceptible to different races prevalent in the region. The lack of information on the genomic regions associated with anthracnose resistance in NW Himalayan common bean population prompted us to dissect Quantitative Resistance Loci (QRLs) against major anthracnose races. In this study, 188 common bean landraces collected from NW region were screened against five important anthracnose races and 113 bean genotypes showed resistance to one or multiple races. Genotyping by sequencing (GBS) was performed on a panel of 192 bean lines (4 controls plus 188 Indian beans) and 22,589 SNPs were obtained that are evenly distributed. Population structure analysis of 192 bean genotypes categorized 188 Indian beans into two major clusters representing Andean and Mesoamerican gene pools with obvious admixtures. Many QRLs associated with anthracnose resistance to Indian C. lindemuthianum virulences (race 3, 87, and 503) are located at Pv04 within the gene models that encode typical resistance gene signatures. The QRLs associated with race 73 are located on Pv08 and overlaps with Co-4 anthracnose resistance gene. A SNP located at distal end of Pv11 in a gene model Phvul.011G202300 which encodes a LRR with a typical NB-ARC domain showed association with race 73 resistance. Common bean genomic regions located at Pv03, Pv09, and Pv11 showed association with resistance to anthracnose race 2047. The present study showed presence of many novel bean genomic regions associated with anthracnose resistance. The presence of Co-4 and Co-2 genes in our material is encouraging for breeding durable anthracnose resistant cultivars for the region.

Genome-Wide Association Study Reveals Genomic Regions Associated with Fusarium Wilt Resistance in Common Bean

“…Gene annotation allowed the identification of candidate genes associated with putative effects in disease-resistance mechanisms (R), such as a cluster of 20 candidate genes annotated as "leucine-rich repeat-containing protein" (LRR), with distances from 0.03 Mb from the Phvul.011G200300 gene up to 0.39 Mb from the Phvul.011G203100 gene positioned close to the ss715648096 marker on Pv11 associated with DSR and AUDPC for UFV01 (Table 4). The region of 51.50 Mb associated with the significant ss715648096 marker on Pv11 corroborates previous studies, and the region being associated with other important fungal diseases of common bean, such as anthracnose, by the association of marker S11_51790295 to race 73 of Colletotrichum lindemuthianum (the anthracnose pathogen), positioned at a distance of approximately 0.20 Mb [112]. The identification of LRR receptor-like protein kinases (PK) and their role in adaptive selection supports prior literature indicating a co-evolution of common bean and the anthracnose fungus [44,113].…”

Common bean as a potential crop for future food security: an overview of past, current and future contributions in genomics, transcriptomics, transgenics and proteomics

“…Hatey et al [204] described ESTs as partial sequences of transcribed genes that represent gene expression in various tissues in which mRNA was obtained in different genotypes. Various studies have been conducted to create cDNA libraries for various legume crops [205][206][207][208] and stated that the number of ESTs currently available for all plant species are more than 21 million [191] mn contents genotype Snp 31 pv01,pv02, pv03, pv05, pv08, pv10, pv11 [191] anthracnose resistance (race 3, 87, and 503) genotype Snp many pv04 (Strongly) [192] anthracnose resistance (race 73) genotype Snp many pv08 (Strongly) [192] [197] sequences. More than 3 million of all sequences have been produced from legumes.…”

Combining disease resistance and postharvest quality traits by early marker-assisted backcrossing in carioca beans

“…Quantitative resistance loci (QRLs) has also been reported and genomic regions associated with important races such as the 3, 4, 9, 38, 55, 65, 73, 87, 503, 2047 and3481 (Banoo et al, 2020;Oblessuc et al, 2014;Perseguini et al, 2016;Vidigal-Filho et al, 2020). Indeed, these Co loci may be part of disease resistance clusters and QRL on all bean chromosomes (from Pv01 to Pv11, Banoo et al, 2020;Campa et al, 2014;Ferreira et al, 2013;Geffroy et al, 2008;Gonçalves-Vidigal et al, 2011;Gonçalves-Vidigal et al, 2012;Gonçalves-Vidigal et al, 2013;Mungalu et al, 2020;Murube et al, 2019;Oblessuc et al, 2014;Perseguini et al, 2016;Richard et al, 2014;Rodríguez-Suárez et al, 2007;Sousa et al, 2014;Vaz Bisneta and Gonçalves-Vidigal, 2020;Vidigal-Filho et al, 2020;Zuiderveen et al, 2016).…”

“…Anthracnose resistance in common bean is governed by monogenic independent genes identified by the Co symbol (Ferreira et al, 2013). Nowadays, there have been found around 25 major ANT resistance genes belonging to the Andean and Mesoamerican gene pools (Banoo et al, 2020;Vaz Bisneta and Gonçalves-Vidigal, 2020).…”